Genetic diversity in - chilli (Capsicum annuum L.) based on microsatellite markers: An evaluation of Bangladeshi germplasm
DOI:
https://doi.org/10.14720/aas.2022.118.4.2511Keywords:
chilli, genetic diversity, microsatellite (SSR) markers, polymorphism information contentAbstract
Genetic diversity analysis is a pre-requisite to develop improve variety of any crop. Hence, 39 SSR markers were used to analyze the genetic diversity of local chilli cultivars. PCR-amplified microsatellite loci were shown to be polymorphic in all investigated cultivars. The locus, CAMS-647 produced the highest number of alleles (8) ranging in size from 188 to 279 bp. PIC values for 39 primers ranged from 0.099 for the locus Hpms 1-165 to 0.806 for the locus CAMS-679. All of the SSRs examined were informative in characterizing the genotypic variance of the samples while 12 were more informative with higher PIC values (> 0.6). There was a wide range of genetic diversity varied from 0.117 (HpmsE075) to 0.806 (CAMS-647), whereas the highest (1.713) and the lowest (0.205) value of Shannon’s Information Index was registered in the locus CAMS-679 and Hpms 1-165, respectively. There was a higher degree of genetic differentiation (0.927) and a lower amount of gene flow (0.010). Nei’s genetic distance (GD) varied from 0.100 to 0.990. Among 96 cultivars, 55 had distinct status in the dendrogram with higher GD values (> 0.6), while 41 cultivars showed a close relationship and yielded lower GD values.
References
Abouzied, H. M., Eldemery, S. M. M., & Abdellatif, K. F. (2013). SSR-based genetic diversity assessment in tetraploid and hexaploid wheat populations. Biotechnology Journal International, 390–404. https://doi.org/10.9734/BBJ/2013/4340 DOI: https://doi.org/10.9734/BBJ/2013/4340
Anumalla, M., Roychowdhury, R., Geda, C. K., Mazid, M., & Rathoure, A. K. (2015). Utilization of plant genetic resources and diversity analysis tools for sustainable crop improvement with special emphasis on rice. International Journal of Advanced Research, 3(3), 1155–1175. https://doi.org/http://www.journalijar.com/article/4175/utilizationofplantgeneticresourcesanddiversityanalysistoolsforsustainablecropimprovementwithspecialemphasisonrice/
BBS. (2021). Statistical Year Book Bangladesh.
Cao, T., Duprez, E., Borden, K. L. B., Freemont, P. S., & Etkin, L. D. (1998). Ret finger protein is a normal component of PML nuclear bodies and interacts directly with PML. Journal of Cell Science, 111(10), 1319–1329. https://doi.org/10.1242/jcs.111.10.1319 DOI: https://doi.org/10.1242/jcs.111.10.1319
Chen, X., Min, D., Yasir, T. A., & Hu, Y. G. (2012). Genetic diversity, population structure and linkage disequilibrium in elite chinese winter wheat investigated with SSR markers. PLoS ONE, 7(9), 1–9. https://doi.org/10.1371/journal.pone.0044510 DOI: https://doi.org/10.1371/journal.pone.0044510
Dhaliwal, M. S., Yadav, A., & Jindal, S. K. (2014). Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers. African Journal of Biotechnology, 13(31), 3137–3143. https://doi.org/10.5897/ajb2014.13695 DOI: https://doi.org/10.5897/AJB2014.13695
Di Dato, F., Parisi, M., Cardi, T., & Tripodi, P. (2015). Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm. Euphytica, 204(1), 103–119. https://doi.org/10.1007/s10681-014-1345-4 DOI: https://doi.org/10.1007/s10681-014-1345-4
Farhad, M., Hasanuzzaman, M., Biswas, B. K., Arifuzzaman, M., & Islam, M. M. (2010). Genetic divergence in chilli (Capsicum annuum L.). Bangladesh Research Publication Journal, 3(3), 1045–1058.
Hernández-Pérez, T., Gómez-García, M. del R., Valverde, M. E., & Paredes-López, O. (2020). Capsicum annuum (hot pepper): An ancient Latin-American crop with outstanding bioactive compounds and nutraceutical potential. A review. Comprehensive Reviews in Food Science and Food Safety, 19(6), 2972–2993. https://doi.org/10.1111/1541-4337.12634 DOI: https://doi.org/10.1111/1541-4337.12634
Hossain, S. M., Habiba, U., Bhuyan, S. I., Haque, M. S., Begum, S. N., & Hossain, D. M. (2014). DNA fingerprinting and genetic diversity analysis of chilli germplasm using microsatellite markers. Biotechnology, 13(4), 174–180. https://doi.org/10.3923/biotech.2014.174.180 DOI: https://doi.org/10.3923/biotech.2014.174.180
Islam, M. N., Molla, M. R., Rohman, M. M., Hasanuzzaman, M., Islam, S. M. N., & Rahman, L. (2012). DNA fingerprinting and genotyping of cotton varieties using SSR markers. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 40(2), 261–265. https://doi.org/10.15835/nbha4028166 DOI: https://doi.org/10.15835/nbha4028166
Islam, M. Z., Khalequzzaman, M., Bashar, M. K., Ivy, N. A., Mian, M. A. K., Pittendrigh, B. R., Haque, M. M., & Ali, M. P. (2018). Variability assessment of aromatic rice germplasm by pheno-genomic traits and population structure analysis. Scientific Reports, 8(1), 1–14. https://doi.org/10.1038/s41598-018-28001-z DOI: https://doi.org/10.1038/s41598-018-28001-z
Jain, S., Kumar, A., Mamidi, S., & McPhee, K. (2014). Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers. Molecular Biotechnology, 56(10), 925–938. https://doi.org/10.1007/s12033-014-9772-y DOI: https://doi.org/10.1007/s12033-014-9772-y
Lee, C. J., Yoo, E. Y., Shin, J., Lee, J., Hwang, H. S., & Kim, B. D. (2005). Erratum: Non-pungent Capsicum contains a deletion in the capsaicinoid synthetase gene, which allows early detection of pungency with SCAR markers (Molecules and Cells 19, 2 (262-267)). Molecules and Cells, 20(2), 303.
Mimura, Y., Inoue, T., Minamiyama, Y., & Kubo, N. (2012). An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. Breeding Science, 62(1), 93–98. https://doi.org/10.1270/jsbbs.62.93 DOI: https://doi.org/10.1270/jsbbs.62.93
Minamiyama, Y., Tsuro, M., & Hirai, M. (2006). An SSR-based linkage map of Capsicum annuum. Molecular Breeding, 18(2), 157–169. https://doi.org/10.1007/s11032-006-9024-3 DOI: https://doi.org/10.1007/s11032-006-9024-3
Molla, K. A., Bhusan, A. B., Ganie, S. A., & Mondal, T. K. (2015). Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.). BMC Plant Biology, 15(1), 1–11. https://doi.org/10.1186/s12870-015-0498-1 DOI: https://doi.org/10.1186/s12870-015-0498-1
Molla, M. R., Ahmed, I., Rahman, S., Hossain, M. A., Salam, M. A., Chowdhury, M. A. Z., & Rohman, M. M. (2017). Genetic diversity among muskmelon (Cucumis melo L.) germplasm in Bangladesh as revealed by microsatellite markers. African Journal of Agricultural Research, 12(44), 3203–3213. https://doi.org/10.5897/ajar2017.12617 DOI: https://doi.org/10.5897/AJAR2017.12617
Molla, M. R., Ahmed, I., Rohman, M. M., Hossain, M. A., & Chowdhury, M. A. Z. (2016). Genetic diversity analysis and DNA fingerprinting of Mungbean (Vigna radiata L.) genotypes using SSR markers. Plant Science, 6(4), 153–164.
Molla, Md Rezwan, Rohman, M. M., Monsur, M. B., Hasanuzzaman, M., & Hassan, L. (2021). Screening and assessment of selected chilli (Capsicum annuum L.) genotypes for drought tolerance at seedling stage. Phyton, 90(5), 1425. https://doi.org/10.32604/phyton.2021.015591 DOI: https://doi.org/10.32604/phyton.2021.015591
Nei, M. (1972). Genetic distance between populations. The American Naturalist, 106(949), 283–292. https://doi.org/10.1086/282771 DOI: https://doi.org/10.1086/282771
Pickersgill, B. (1991). Cytogenetics and evolution of Capsicum L. In: Tsuchiya T, Gupta PK (Editors), Chromosome Engineering in Plants: Genetics, Breeding, Evolution Part B. Elsevier, Amsterdam. pp. 139-160. https://doi.org/10.1016/B978-0-444-88260-8.50013-6 DOI: https://doi.org/10.1016/B978-0-444-88260-8.50013-6
Rahman, M., Sohag, M., & Rahman, L. (2010). Microsatellite based DNA fingerprinting of 28 local rice (Oryza sativa L.) varieties of Bangladesh. Journal of the Bangladesh Agricultural University, 8(1), 7–17. https://doi.org/10.3329/jbau.v8i1.6391 DOI: https://doi.org/10.3329/jbau.v8i1.6391
Roychowdhury, R., Taoutaou, A., Hakeem, K. R., Ragab, M., Gawwad, A., & Tah, J. (2014). Molecular Marker-Assisted Technologies for Crop Improvement. In Crop improvement in the era of climate change (Vol. 2, Issue April 2016, pp. 241–258). https://doi.org/10.13140/RG.2.1.2822.2560
Saghai-Maroof, M. A., Soliman, K. M., Jorgensen, R. A., & Allard, R. W. (1984). Ribosomal DNA spacer-length polymorphisms in barley : Mendelian inheritance , chromosomal location , and population dynamics. Proceedings of National Academy Science, 81(December), 8014–8018. https://doi.org/10.1073/pnas.81.24.8014 DOI: https://doi.org/10.1073/pnas.81.24.8014
Sharmin, A., Hoque, M. E., Haque, M. M., & Khatun, F. (2018). Molecular diversity analysis of some chilli (Capsicum spp.) genotypes using SSR markers. American Journal of Plant Sciences, 09(03), 368–379. https://doi.org/10.4236/ajps.2018.93029 DOI: https://doi.org/10.4236/ajps.2018.93029
Sundaram, R. M., Naveenkumar, B., Biradar, S. K., Balachandran, S. M., Mishra, B., Ilyasahmed, M., Viraktamath, B. C., Ramesha, M. S., & Sarma, N. P. (2008). Identification of informative SSR markers capable of distinguishing hybrid rice parental lines and their utilization in seed purity assessment. Euphytica, 163(2), 215–224. https://doi.org/10.1007/s10681-007-9630-0 DOI: https://doi.org/10.1007/s10681-007-9630-0
van Zonneveld, M., Scheldeman, X., Escribano, P., Viruel, M. A., van Damme, P., Garcia, W., Tapia, C., Romero, J., Sigueñas, M., & Hormaza, J. I. (2012). Mapping genetic diversity of cherimoya (Annona cherimola Mill.): Application of spatial analysis for conservation and use of plant genetic resources. PLoS ONE, 7(1). https://doi.org/10.1371/journal.pone.0029845 DOI: https://doi.org/10.1371/journal.pone.0029845
Yi, G., Lee, J. M., Lee, S., Choi, D., & Kim, B. D. (2006). Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theoretical and Applied Genetics, 114(1), 113–130. https://doi.org/10.1007/s00122-006-0415-y DOI: https://doi.org/10.1007/s00122-006-0415-y
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Copyright (c) 2022 Md. Rezwan MOLLA, Iftekhar AHMED, Md. Motiar ROHMAN, Mohammad Amdadul HAQUE, Shah Md. Monir HOSSAIN, Lutful HASSAN
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